Soil compaction is an increasing environmental threat due to agricultural intensification. Compaction negatively affects both agricultural production and key soil environmental functions. In this study, we developed a novel soil-compaction-agroecosystem modelling framework to systematically assess the consequences of soil compaction on crop yield, soil organic carbon stocks, nitrous oxide emissions and nitrogen leaching in the long-term. The modelling was done for different soil textures, different climatic conditions and different soil structure recovery rates, each of them tested comprising three cases. We compared simulations with data from field observations compiled from the literature. The modelling results reproduced most trends reported in the literature. Comparing compacted vs. non-compacted simulations, the accumulated effects over a 20 year-long period caused by a single wheeling event (two axle passes with 8 Mg wheel load) on a loamy soil without soil structure recovery and weather conditions of central Europe were estimated to account for an accumulated loss of about 21 Mg ha−1 in cereal grain yield, a decrease of nearly 1.8% in soil organic carbon (corresponding to a loss of about 1 Mg ha−1), an increase of 130% in nitrous oxide emissions (about 0.5 kg ha−1 annual increase) and an increase of 15% in nitrate leaching (annual increase of approximately 8 kg ha−1). This work offers a novel approach for accounting for effects of compaction on interacting soil processes and enables the quantification of long-term adverse impacts of soil compaction on key soil ecosystem services across diverse pedoclimatic conditions, thereby providing a scientific basis for the design of effective mitigation strategies.